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1 process TOP_UNIQUE_SEROVARS {
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2 tag "$meta.id"
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3 label "process_pico"
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4 maxForks 5
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5
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6 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
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7 conda (params.enable_conda ? "conda-forge::python=3.10.4" : null)
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8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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9 'https://depot.galaxyproject.org/singularity/python:3.10.4' :
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10 'quay.io/biocontainers/python:3.10.4' }"
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11
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12 input:
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13 tuple val(meta), path(mash_screen_res)
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14
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15 output:
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16 tuple val(meta), path('*_UNIQUE_HITS.txt') , emit: tsv, optional: true
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17 tuple val(meta), path('*_UNIQUE_HITS_POPUP.txt'), emit: popup, optional: true
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18 tuple val(meta), path('*_UNIQUE_HITS_ACCS.txt') , emit: accessions, optional: true
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19 tuple val(meta), path('*_UNIQUE_HITS.fna.gz') , emit: genomes_fasta, optional: true
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20 path'*FAILED.txt' , emit: failed, optional: true
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21 path 'versions.yml' , emit: versions
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22
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23 when:
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24 task.ext.when == null || task.ext.when
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25
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26 script:
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27 def args = task.ext.args ?: ''
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28 def prefix = task.ext.prefix ?: "${meta.id}"
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29 args += (mash_screen_res ? " -m ${mash_screen_res}" : '')
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30 args += (prefix ? " -op ${prefix}" : '')
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31 """
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32 get_top_unique_mash_hit_genomes.py \\
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33 $args
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34
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35 cat <<-END_VERSIONS > versions.yml
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36 "${task.process}":
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37 python: \$( python --version | sed 's/Python //g' )
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38 datasets: \$( datasets --version | sed 's/datasets version: //g' )
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39 dataformat: \$( dataformat version )
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40 END_VERSIONS
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41 """
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42
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43 } |
